I had broken metadata on this db, so I unlink my db and now trying to link it back, but not sure if it will be safe, will this clean all metadata from prev sc ??

On setup page I see that Linking db will <Link the database and Commit the objects>.
Does it mean that If I don't have let say usp_AlphaBravo in my BAK copy this copy will be deleted from SC depo when I do Linking? This sound scary for me....

Yes, we put in the basic folder structure and the RedGate.ssc file when you first link- so the #ignorepolicies is needed for that to succeed. From then on you need to either add a comment or the above #ignore command